title: Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS.
abstract: OxyS and RprA are two small noncoding RNAs (sRNAs) that modulate the expression of rpoS, encoding an alternative sigma factor that activates transcription of multiple Escherichia coli stress-response genes. While RprA activates rpoS for translation, OxyS down-regulates the transcript. Crucially, the RNA binding protein Hfq is required for both sRNAs to function, although the specific role played by Hfq remains unclear. We have investigated RprA and OxyS interactions with Hfq using biochemical and biophysical approaches. In particular, we have obtained the molecular envelopes of the Hfq-sRNA complexes using small-angle scattering methods, which reveal key molecular details. These data indicate that Hfq does not substantially change shape upon complex formation, whereas the sRNAs do. We link the impact of Hfq binding, and the sRNA structural changes induced, to transcript stability with respect to RNase E degradation. In light of these findings, we discuss the role of Hfq in the opposing regulatory functions played by RprA and OxyS in rpoS regulation.
authors.affiliation: Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom.
authors.forename: Charlotte A
authors.initials: CA
authors.lastname: Henderson
authors.forename: Helen A
authors.initials: HA
authors.lastname: Vincent
authors.forename: Alessandra
authors.initials: A
authors.lastname: Casamento
authors.forename: Carlanne M
authors.initials: CM
authors.lastname: Stone
authors.forename: Jack O
authors.initials: JO
authors.lastname: Phillips
authors.forename: Peter D
authors.initials: PD
authors.lastname: Cary
authors.forename: Frank
authors.initials: F
authors.lastname: Sobott
authors.forename: Darren M
authors.initials: DM
authors.lastname: Gowers
authors.forename: James E N
authors.initials: JEN
authors.lastname: Taylor
authors.forename: Anastasia J
authors.initials: AJ
authors.lastname: Callaghan
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D055592:Biophysical Phenomena; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020836:Protein Structure, Quaternary; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D053838:Scattering, Small Angle; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D012097:Repressor Proteins; D012808:Sigma Factor; C499686:oxyS small RNA, E coli; C069567:sigma factor KatF protein, Bacteria
keywords: Hfq; OxyS; RprA; rpoS; sRNA